The government shutdown over passage of the Patient Protection and Affordable Care Act has led to suspension of normal activities by many agencies overseen by HHS; service agencies will remain largely unaffected, but grant-making, employee-intensive and research agencies, including the Agency for Healthcare Research and Quality, Centers for Disease Control and National Institutes of Health, will operate at a much reduced capacity, according to HHS' contingency staffing plan for operations in the absence of enacted annual appropriations.

HHS' staffing plan indicates that AHRQ will experience substantial furlough. AHRQ will stop funding grants and contracts for health research, including research on patient safety and healthcare-associated infection reduction. The agency will also cease data collection for the Medical Expenditure Panel Survey.

AHRQ will continue Patient-Centered Outcomes Research Trust Fund projects and CMS-funded measure development for the Children's Health Insurance Program Reauthorization Act.

CDC will no longer support its seasonal influenza program, including outbreak detection and epidemiological tracking of the influenza virus. It will also stop updating disease treatment and prevention guidelines and recommendations and will no longer support states in disease surveillance or analysis.

CDC will continue to process laboratory samples and will maintain its 24/7 emergency operations center. Any activities with mandatory funding, including global AIDS programs and a few programs related to childhood obesity reduction, will also continue.

NIH will not admit new patients unless personally approved by the NIH Director due to medical necessity. The agency will also stop issuing new protocols and will not take action on any grant applications or awards.

The NIH will continue patient care for patients at its NIH Clinical Center and will provide minimal support for ongoing protocols and animal care as well as facility and infrastructure protection.

CMS will be largely unaffected by the government shutdown, and all insurance marketplace activities will proceed as planned. However, CMS will not continue investigations into healthcare fraud and abuse, and it will reduce the number of recertification surveys it offers for Medicare an Medicaid providers.

Approximately 40,500 of HHS' nearly 80,000 staff will be placed on furlough until further notice, according to the staffing plan.